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README.md

P-value Weighting R Package

Introduction

This R package contains p-value weighting methods for multiple hypothesis testing. These statistical methods are used for improving power in multiple testing via the use of prior information. The iGWAS method is provided for applications of p-value weighting in Genome-Wide Association Studies.

Some of these methods were were developed by the authors in the following paper: Optimal Multiple Testing Under a Gaussian Prior on the Effect Sizes by Dobriban, Fortney, Kim, Owen: http://arxiv.org/abs/1504.02935, published in Biometrika (2015)

An Example

Suppose we want to find the significant effects in a large pool of candidates, by performing multiple testing with the p-values P_current. We have some prior information about the size of each effect size in the form of prior test statistics t1 with estimated variances sigma. The prior effects t1 with standard errors sigma are our prior guesses for the current effects.

To use this information for improving power in multiple hypothesis testing, we can give each hypothesis a different weight. For instance, we can compute the Bayes p-value weights w, and use them to weight the current p-values P_weighted as follows:

w <- bayes_weights(t1,sigma,q)$w
P_weighted <- P_current/w

Finally, we perform weighted Bonferroni multiple testing, controlling the Family-Wise Error Rate, in the usual way:

P_w_adjusted <- p.adjust(P_weighted,"bonferroni")

Please see the vignette or the help files for examples and a description of the methods.

Installation instructions

To install from GitHub, make sure that Hadley Wickham's devtools (https://github.com/hadley/devtools) is installed, then run:

devtools::install_github("dobriban/pweight")

The package was also available from CRAN, but has been archived.

Main components

The core of the package consists of the following p-value weighting methods, whose details are described in the documentation:

  • Spjotvoll weights: spjotvoll_weights()
  • Exponential weights: exponential_weights()
  • Bayes weights: bayes_weights()

The iGWAS method, iGWAS(), is provided for applications of p-value weighting in Genome-Wide Association Studies.

Please contact the authors if you have any questions.

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